Call variants from a BAM file using iVar
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
A sorted (with samtools sort) and trimmed (with iVar trim) bam file
The reference sequence used for mapping and generating the BAM file
The index for the reference sequence used for mapping and generating the BAM file
A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
Save mpileup file generated by ivar variants
iVar generated TSV file with the variants
mpileup output from samtools mpileup [OPTIONAL]
File containing software versions
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.